Structure of DUB complex

Experimental Data Snapshot

  • Resolution: 3.33 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7.

Lamberto, I.Liu, X.Seo, H.S.Schauer, N.J.Iacob, R.E.Hu, W.Das, D.Mikhailova, T.Weisberg, E.L.Engen, J.R.Anderson, K.C.Chauhan, D.Dhe-Paganon, S.Buhrlage, S.J.

(2017) Cell Chem Biol 24: 1490-1500.e11

  • DOI: https://doi.org/10.1016/j.chembiol.2017.09.003
  • Primary Citation of Related Structures:  
    5VS6, 5VSB, 5VSK

  • PubMed Abstract: 

    Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.

  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7
A, B
353Homo sapiensMutation(s): 0 
Gene Names: USP7HAUSP
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
PHAROS:  Q93009
GTEx:  ENSG00000187555 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93009
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.33 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.39α = 90
b = 69.63β = 99.16
c = 77.97γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references